sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6f221925deffcf07051c6aa497099f9419fb11d2d4530e9df0f4b0d43caad397 | MATLAB | 2,517 | 84 | function [gx,dG_dX,dG_dPhi] = g_fullDCM4fmri(Xt,Phi,ut,inG)
% full DCM observation function (embedding dynamic Ballon model)
% function [gx,dG_dX,dG_dPhi] = g_fullDCM4fmri(Xt,Phi,ut,inG)
% This function evaluates the observation function of the neuronal level in
% DCM for fMRI. Note that this "generalized" observation... |
7244898bd427e859f19f47e66af8520d3dc02e354f542bd7444574b4d747ec5c | MATLAB | 2,517 | 82 | function Draw_ROIs_on_Cortex(Anat,ROI)
%
% This function will draw ROI spheres on a model of the cortical surface.
% Anat is a structure that describes the anatomy.
% ROI is a structure that describes the regions of interest.
%
% Anat fields:
% CtxL mesh for left cortex. mesh includes 2 fields, nodes and
% ... |
01629be0ee705ca077930a70569a795e616e02e47e1174b18ac4024911e07e6c | MATLAB | 2,518 | 76 | % Code taken from Paul Scovanner's homepage:
% http://www.cs.ucf.edu/~pscovann/
% Calculate 3D Sift
% img is the input in question.
% keypts is an Nx3 matrix of keypoints
function keys = calculate_3DSIFT(img, keypts,skipDescriptor)
%By default, we calculate the descriptor
if nargin<3
skipDescriptor=false;
end... |
05a7b9206eb44d192e74aeb1b884a8a6c66ee9831c11446be97124056dce4256 | MATLAB | 2,518 | 55 | function isom = calcIsomPerWatt(deviceSpectrum, photoreceptorSpectrum)
%CALCISOMPERWATT Calculates the rate of photoreceptor isomerizations per watt.
% This function computes the isomerization rate (isom) in photoreceptors
% induced by a given light source, integrating the product of the device's
% spectral power distr... |
0dd81e9521cca63add4fb8d739b14d7bfec5fb2ee7b0e958e8d358e2a6f000cd | MATLAB | 2,519 | 68 | function [dat] = read_nihonkohden_m00(filename, begsample, endsample)
% READ_NIHONKOHDEN_M00 reads data Nihon Kohden EEG system and converts the
% floating point ASCII values to 16-bit signed integers from *.m00 file
% format. This function is an adaptation of convert_nkascii2mat.m written
% by Timothy Ellmore
%
% Use... |
f078a5a82938b72801f5f50c87149c30d79e9987bd427cb0e02a338c538ab28c | MATLAB | 2,519 | 80 | clear;clc;
%% parameters
% -2e-3,-2e-3
% -2e-3,2e-3
params = struct('a',1.6e-2,'n',4,'beta',10,...
'ind_input',[11],'ind_output',[13,14],...
'u_input',[0,-0.005*9.8],'u_output',[0,1;0,0]);
[DT,bonds] = Triangle(params);
n_spring = size(bonds,1);
w1 = 1.5*10^(-3);w2 = 2.5*10^(-3);
thickness = 2*10^(-3);
Y = 5.5... |
e0b6a4392db7c646f7fccf848debeca7003728d2a418e3f86d74d72a16b10646 | MATLAB | 2,520 | 90 | function simulatedAnnealingDemo2d()
[XX, YY]=meshgrid(1:49,1:49);
f = exp(-energySurface); % 49x49 grid
% find maximum peak by exhaustive search
M = max(f(:)); % 8.0752
[row,col] = find(f==M); % max row 38, col 25
fprintf('Search: max height = %5.3f at (%d, %d)\n', M, row, col);
% simulated annealing
setSeed(2);
x... |
f11d1037c53847ffedb38f7a38fe98f86825f9bae74673a5f35f29e6fd833bd6 | MATLAB | 2,520 | 73 | % PadContinuousData.m
% Sarah West
% 8/4/22
% Pads continuous data to have speed, accel, duration, pupil diameter in
% first - 4th entries of data, respectively.
function [parameters] = PadContinuousData(parameters)
MessageToUser('Padding ', parameters);
% Make default empty data padded output = data.
... |
47a9bddcdb26a66d20d14602b2035d096552efb2efa432bcb2599a12b40df29e | MATLAB | 2,521 | 68 | function visualizeGridPlot(puncta,transcript_object,params,fignum)
figure(fignum);
clf('reset')
ha = tight_subplot(params.NUM_ROUNDS,params.NUM_CHANNELS+1,zeros(params.NUM_ROUNDS,2)+.01);
subplot_idx = 1;
for exp_idx = 1:params.NUM_ROUNDS
punctaset_perround = squeeze... |
a0da9fc121501bed8b925c0686ae470218e7d4b0aa0e0cc071dcde1b07be22f9 | MATLAB | 2,521 | 91 | function swave=smoothwavelet(wave,dt,period,dj,scale)
% Smoothing as in the appendix of Torrence and Webster "Inter decadal changes in the ENSO-Monsoon System" 1998
%
% used in wavelet coherence calculations
%
%
% Only applicable for the Morlet wavelet.
%
% (C) Aslak Grinsted 2002-2005
%
% -------------------------... |
ffa32b31d99dd0cf6880b52de1804db1ea76322df4dfd10e32bd97a6e4338657 | MATLAB | 2,521 | 95 | % darkgreen and purple go together
function out_color= get_color(col_name)
if ~exist('col_name', 'var')
co= get(gca, 'colororder');
col_num= get(gca, 'ColorOrderIndex');
out_color= co(col_num+1, :);
elseif ischar(col_name)
switch col_name
case {'r', 'red'}
out_color... |
2c66b4e6d6b28b14d34373254066e05db7bfff5e3dadb41acbec9ec9e24edcdc | MATLAB | 2,523 | 94 | function [data_out,scales_out]=mri2mristandardori(data,ori,scales);
%
% transforms MRI-tensor data
% into standard form, i.e. first index is
% from right to left ear, second index from
% front to back, and 3rd index from bottom to top.
%
% INPUT:
% ori is a vector containing the 3 numbers 1,2, 3
% (eventually also... |
ee5080735a12d367dee4e4403762e68b170a5f5f209264781dc71fd36cba11c8 | MATLAB | 2,523 | 42 | function doc_log_likelihood = CBIG_EM_doc_log_likelihood_wc(w, paradigm, params, q)
% doc_log_likelihood = CBIG_EM_doc_log_likelihood_wc(w, paradigm, params, q)
%
% Compute log likelihood of a single experiment (document) given the updated auxillary parameter q.
% Note that compared to CBIG_EM_doc_log_likelihood_wc.... |
292b9728902c3b7a462840409e0172c5d5261fb0755089185232e64af895f762 | MATLAB | 2,524 | 71 |
% Handling for probability data/Samplings
% common uses for the pxtDataCell, sdoMat, any use of the stirpd estimation
%_______________________________________
% Copyright (C) 2024 Trevor S. Smith
% Drexel University College of Medicine
%
% This program is free software: you can redistribute it and/or modify
% it und... |
dd86849a8258dcd4dbd605ae02947ecea0f790f844f8d4e601c6e02b57d02fc4 | MATLAB | 2,524 | 50 | function [gx,gy_blips,gx_pre,gy_pre,gy_blip_up,gy_blip_down,adc,params] = create_epi_adc_pulseq(params)
lims = params.gen.lims;
gy_pre_area = -(params.gen.del_k(2)*params.gen.n(2)/2/params.epi.ry)*params.epi.pf;
if params.epi.pf ~= 1; gy_pre_area = gy_pre_area+(gy_pre_area/4*-1); end
gy_pre = mr.... |
6f46bc7cc7097dd67a032ba42ed067b3ee6f9287b623d2906c323b8f6fc5e0b7 | MATLAB | 2,525 | 76 | %{
Copyright (c) 2025 Axion BioSystems, Inc.
Contact: support@axion-biosystems.com
All Rights Reserved
%}
classdef LedPosition
%CHANNELMAPPING represents the Position and color of an LED on an
%optical stimulation device.
%
% WellRow: Numeric representation of the well row (e.g.... |
e4019097c67695981536056393b40253845456b5279d62a163683dff1bc7f3c9 | MATLAB | 2,525 | 84 | function data = load_data( filename, options )
% *SPONTANOEUS WAVES DEMO*
%
% LOAD DATA load LFP and spikes from SNL-R Utah array recordings
%
% INPUT
% filename - /path/to/file
% options - options structure (cf. spontaneous_waves_demo.m)
%
% OUTPUT
% data(trial).x - datacube (rows,cols,timepts)
% data(trial).spike... |
e4c1e51cdd6dec61017f10dc460e1ee922e2cda29878b4c52b6bc5c70b9febff | MATLAB | 2,525 | 88 | % RSKELF_SPDIAG Extract diagonal using recursive skeletonization factorization
% via sparse apply/solves.
%
% This algorithm computes each diagonal entry by multiplying from the left
% and right by unit coordinate vectors, taking advantage of the sparsity of
% each such operation.
%
% Typica... |
6e5db77fdd4e1f7f89af7ab8621d915cbd726a646e1b9b1850580dbbf467df50 | MATLAB | 2,526 | 77 | function [rho] = SourceAdvecDiff(rho0,u,r,nt,dt,par)
% Created by Xinan Chen
% This function returns the dynamic intensity rho(:,1~nt) following PDE
% rho_t + grad(rho*u) = sigma*Laplacian(rho) + rho*r*K
% rho(:,0) = rho0
% if K (chi) is not loaded, then assume K = identity
%% rho(:,1...T) = transport (rho0 - initial ... |
a3b39adaf29b72788939bf21dfe8b2f50784ea1d2d0510d2783495b91ea423d0 | MATLAB | 2,526 | 86 | function [datacomp, minres2, bestiter, minconc2, mincomp2, minconc22, ...
number_of_comp, List_of_Max_W, res_spec] = unmixing_components(numflur, wl, Y, iterations, fixedSpec)
% Initialization and setting optimization parameters
Y(isnan(Y)) = 0;
opt = statset('Maxiter', 5000, 'Display', 'iter', 'TolX', 1e-6);
min... |
87c376c475da03c6fb5ea0f5df5e4ae3691bec3bfc83cabcf58ab85bab753ffc | MATLAB | 2,527 | 80 | function [frac_overlap,nnz1_all,nnz2_all] = analyze_AB_synapse_coloc(params,roi,chs)
%created by M.E. Schroeder on 7/27/23
%calculates fraction of mutually overlapping volume for specified synaptic
%and beta-amyloid channels WITHIN cropped beta-amyloid nanoclusters
%calculates the fraction of channel 1 volume mutually ... |
9aec937e44f240038f52b73f26e01a99fc51976cac2eba025b63d1e55695ec93 | MATLAB | 2,527 | 49 | % Statistical Parametric Mapping
% Version 7771 (SPM12) 13-Jan-20
%__________________________________________________________________________
% ___ ____ __ __
% / __)( _ \( \/ )
% \__ \ )___/ ) ( Statistical Parametric Mapping
% (___/(__) (_/\/\_) SPM - https://www.fil.ion.ucl.ac.uk/spm/
%______________... |
0f2e89397109ac97559b7a13b600babfae7fb4ea14009e544682c15f948bd255 | MATLAB | 2,528 | 118 | function m=plotMarker(ind,LM)
% plotMarker -- provide different marker
% function m=plotMarker(ind)
%
% [Inputs]
% ind: index for differnt marker
% LM: index for line/marker change order (default=1: line fixed marker change)
%
% [Outputs]
% m:marker
%
%
%
% Tomoyasu Horikawa horikawa-t@atr.jp 2012/11/28
%
if ~ex... |
456bab49a9679291265461564dac8148f3836ea95bb29644d8fc135fdabf27eb | MATLAB | 2,529 | 92 | function [CenterOfMass] = y_CenterOfMass_Surf(AtlasFile, SurfFile)
% function [CenterOfMass] = y_CenterOfMass_Surf(AtlasFile, SurfFile)
% Extract Eccentric Center of mass on surface
% Input:
% AtlasFile - the Atlas File
% SurfFile - the Surface File
% Output:
% CenterOfMass - the Altals region table
%____________... |
30e947db2a4f94bca214d94053bf1e23fef1f92fbc735eee92aa56fb1e33fc1f | MATLAB | 2,530 | 106 | %% parameters
x0 = 0;
y0 = 0;
theta0 = 0;
T = 1000;
dampen_pos = .25;
dampen_theta = .5;
sigma_pos = 10;
sigma_theta = .05;
% these are the parameters I use for tracking flies
velocity_angle_weight = .03;
max_velocity_angle_weight = .18;
%% initialize
x = nan(1,T);
y = nan(1,T);
theta = nan(1,T);
x(1) = x0;
y(1) =... |
59e5e0f93c80f34b8320d67db958a4c4efd3505b532b031ac68bb89e4e852646 | MATLAB | 2,530 | 125 | function event = read_micromed_event(trcfile)
% reads the events of the Micromed TRC format files
fid=fopen(trcfile,'r');
%------------------reading patient & recording info----------
fseek(fid,64,-1);
surname=char(fread(fid,22,'char'))';
name=char(fread(fid,20,'char'))';
fseek(fid,128,-1);
day=fread(fid,1,'char');... |
a238aa9728cf7d90485a3e8b08bcb4bf2e74397dab43a3eb2b1152b5a6a3e480 | MATLAB | 2,530 | 60 | function [ titlestr, settings, results ] = createNNGraphFromLabels( dataview, settings )
% Creates a nearest neighbour graph based on the given labels.
%
% This graph is computed using the Euclidean distance.
%
% See also dspace_graphs.RealtimeLabelBasedNNGraph.
%
%
%
%<PRE>
... |
2d2c3566e45aae90b9f4d6312088bbf279bf5e0d4671748c2cb010ee37087929 | MATLAB | 2,531 | 77 | % Purpose: Calculate network for each MS-HBM network
% Inputs: Hungarian-matched individual network parcellations
% Outputs: rh_labels and lh_labels containing overlap values for
% each network
%
% Written by M. Peterson, Nielsen Brain and Behavior Lab, under MIT License
% 2024
% To run:
% 1. Claim computing resourc... |
522855b96356ec7eea2f60fd1482622e20e67e37f8de37fe9043ac4e8c3600a0 | MATLAB | 2,531 | 172 | clear
clc
close all
rat='P100';
rat=rat(2:end);
rat=str2double(rat);
load data/combined_kernels.mat
%%% (generated by combine_neural_kernels.m)
data=data_all_trials;
data.centers=-1:0.02:2;
vecx=0.01:0.02:0.66;
data.vecx=vecx;
load data/rat_for_each_neuron
ind=find(rat_numbers==rat);
wddall=data.glm_dd(... |
3b87687683b4f31958d0b7f1e8c2d4428eec4a24f28ec9120dfd0827e5b2778b | MATLAB | 2,532 | 85 | function [scan_ids, subj_ids, subj_info, tab_hdr] = read_subject_ids(subj_file, varargin)
% _
% Read Scanner IDs and Subject IDs from Excel file
%
% subj_file - an XLS or TXT file containing subject information
% property - (optional) property to select sub-set of subjects
% value - (optional) propert... |
95d2211e0884415d0cb36261e746d1d40b57fc41b0ed5bee470264f32ee1474a | MATLAB | 2,532 | 79 | function [varargout] = splint_gh(varargin)
% SPLINT_GH implements equations (3) and (5b) of Perrin 1989
% for simultaneous computation of multiple values
% Copyright (C) 2004-2009, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% Fie... |
da32374184f3cd6c33749c517b77ff5247c68995956d3a8f0a8dba70da09c8d0 | MATLAB | 2,532 | 64 | function [s_Trans, s_Rotation, s_Scale, s_Shear]=affine_parameter_scaling(sizeI)
% This function gives scaling values for different parameters, such as
% rotation and shear of an affine matrix. This scaling make the influence on
% pixel changes in registration of for instance a rotation value
% approximately equal ... |
dc73ed283d5b71e447da7f30324d8b6470ca4dff68d1e3df6a53cb7861e1fe42 | MATLAB | 2,532 | 75 | function [xyz,T,ypr,Uo,Vo,Z] = DLTcameraPosition(coefs)
% function [xyz,T,ypr,Uo,Vo,Z] = DLTcameraPosition(coefs)
%
% Computes the camera position in the calibration frame coordinate system.
% This is useful because it allows you to recreate the scene perceived by
% the camera in a 3D modeling and animation prog... |
ebcd78a43661fe079370b66d18c40dc925db075068fa0c8fc6e813ffe7a528b4 | MATLAB | 2,532 | 90 | % meg_runAnalysisMultiSession
%% Setup
expt = 'TA2';
% sessionDirs = {'R0817_20181120','R0817_20190625'};
sessionDirs = {'R1187_20181119','R1187_20190703'};
user = 'mcq';
paramType = 'Analysis';
% params
p = meg_params(sprintf('%s_%s', expt, paramType));
nSessions = numel(sessionDirs);
saveAnalysis = 0;
saveFigs = ... |
13cd89cee3c05e2446aea984dc7b3e0fa1732110a9a48e2fcb42f10ecc667f23 | MATLAB | 2,533 | 105 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
389458def005ae314d24824d17594d0404baf05b61ee3877dec3a0b9946c52e2 | MATLAB | 2,533 | 71 | function [ut] = svdfft_c(c, n, trltapcnt);
% SVDFFT computes a rotated FFT matrix, using the real part of the
% cross-spectral density matrix. This rotation ensures that the phase
% relationship of the underlying sources does not change, while rotating
% the channels such that the first channel contains the maximal am... |
7cb30127171414644998213b1f5def872e4b36c28ce61134b631038a822ebec1 | MATLAB | 2,533 | 80 | function [nrm] = normals(pnt, tri, opt)
% NORMALS compute the surface normals of a triangular mesh
% for each triangle or for each vertex
%
% [nrm] = normals(pnt, tri, opt)
% where opt is either 'vertex' or 'triangle'
% Copyright (C) 2002-2007, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fiel... |
3551e3900a0fb65038d3c906546b5ff2246bc8aa0764e1f7160e2517c0ac3c0e | MATLAB | 2,534 | 53 | function cellmdl = paramsToStructFlicker(mdlparams, gridcent, ktbas, dgrid, multfac)
%PARAMS_TO_STRUCT_FLICKER Converts model parameters to a structured format for flicker stimuli.
%
% This function takes a vector of model parameters (mdlparams),
% information about the subunit grid (gridcent, dgrid), temporal
% ... |
645f49ed583ae1f14108d199abd851ad696bf2a451786062b6942371c5298283 | MATLAB | 2,534 | 60 | function params = prepare_add_parameters(seq,ks_traj,gx,rf,adc,te0,te1,tr0,tr1,params)
% Update resolution and mtx size with effective resolution
rx = 1./(abs(max(ks_traj.kx(:,1)))+abs(min(ks_traj.kx(:,1))));
if params.gen.ro_type == 'c'
ry = 1./(abs(max(ks_traj.ky(:,1)))*2);
else
ry = ... |
3e46cee9711a7f26887d3ccb2faf41ded121114786371a01d020f0ef14cf1688 | MATLAB | 2,536 | 92 | loadExperimentParams;
% LOAD IMG VOLUME
filename = fullfile(params.INPUTDIR,sprintf('%sround%d_%s.tif',...
params.SAMPLE_NAME,params.MOVING_RUN,params.REGISTERCHANNEL));
img = load3DTif(filename);
% LOAD KEYS
output_keys_filename = fullfile(params.OUTPUTDIR,sprintf('globalkeys_%sround%d.mat',params.SAMPLE_NAME,p... |
84d286554e07cd2098ae3e5e0ac432f7547087eaff011c935241e3c53750a861 | MATLAB | 2,536 | 96 | %load net;
load('results_training.mat');
rng(0);
%% Evaluation of the network
%https://es.mathworks.com/help/vision/ug/semantic-segmentation-using-deep-learning.html
%% Calculated over all images:
pxdsResults = semanticseg(imds,net, ...
'MiniBatchSize',20, ...
'WriteLocation',tempdir, ...
'Verbose',false)... |
18b4f3dc7678654ef50e6f1bcbd873e6004022cfd5dd79515baa2f03d0983969 | MATLAB | 2,537 | 81 | function stats=ModularityHSB(clrs,rmat0,rth,params)
%
% This function calculates the modularity for a set of clustering
% assignments for a given rmatrix. This metric is based on Newman, 2004.
% It is assumed that the clrs per kden/rth are along each column on clrs.
% Ignore modules set to zero (unclassified).
... |
25478b7fae94664982ef26fcf4174c46c9d604be8621a0497880bf75f4cd00b4 | MATLAB | 2,537 | 73 | function strainStruct = metricStrainFromG(M)
% get a strain structure from the metric at a point
%
% metricStrainFromG(M)
%
% M: 2x2 matrix
%---------------------------------------------------------------------
% license
%----------------------------------------------------------... |
3c32aab362dd46fc5cb79dbf4da400704c4ab02b7882673efe31eb361358cf02 | MATLAB | 2,537 | 69 | function h_dragZoomInBox3
point1 = get(gca,'CurrentPoint'); % button down detected
point1 = point1(1,1:2); % extract x and y
%
% roiobj = findobj(gcf,'Tag','HROI');
% set(roiobj, 'Selected','off');
% bgroiobj = findobj(gcf,'Tag','HBGROI');
% set(bgroiobj, 'Selected','off');
% % roeobj = findobj(... |
91894d982f761f7e1acaefc328e831fdd08fa49058a323cfbfd5ed9db439d0ed | MATLAB | 2,537 | 84 | %% Test for run_main.m
% Setup
clear;
basefolder = fileparts(fileparts(mfilename('fullpath')));
codefolder = [basefolder,'/code'];
toolsfolder = [basefolder,'/tests/tools'];
addpath(genpath(codefolder));
addpath(genpath(toolsfolder));
% Setup needed variables and test if it fails without them
testError(@() rmain(... |
b929aff9c465030e52b5022f235b662c13e789af68cfc3b3c1ba2720ad10190c | MATLAB | 2,537 | 97 | % SOFA API - test script
% Test some of the SOFA API functionality
% Copyright (C) 2012-2013 Acoustics Research Institute - Austrian Academy of Sciences
% Licensed under the EUPL, Version 1.1 or – as soon they will be approved by the European Commission - subsequent versions of the EUPL (the "License")
% You may not u... |
5441156f0812b98d7aa03b5545875f6f5c403df2a48abd9ce812d453f81156ba | MATLAB | 2,538 | 76 | function CBIG_ASDf_mean2mat(inputDir, outputDir, k, r, scalelim)
% CBIG_ASDf_mean2mat(inputDir, outputDir, k, r, scalelim)
%
% This function computes factor-specific RSFC patterns (i.e., E(RSFC patterns|Factor)),
% plot it and save it as a 419x419 matrix.
%
% Input:
% - inputDir:
% Absolute path to the d... |
84a80ca5a0c150dd5eb47db2a795054e8f92d8d049df8fde9c8648ade4196966 | MATLAB | 2,538 | 179 | clear
clc
close all
rat='P049';
rat=rat(2:end);
rat=str2double(rat);
load data/combined_kernels.mat
%%% (generated by combine_neural_kernels.m)
data=data_all_trials;
data.centers=-1:0.02:2;
vecx=0.01:0.02:0.66;
data.vecx=vecx;
load data/rat_for_each_neuron
ind=find(rat_numbers==rat);
wddall=data.glm_... |
c08cfb4fa62e91b3baf10733498e01a51f71b37a12518de91993917e3e864c1c | MATLAB | 2,539 | 83 | function redrawCuboidSurfaces(src,~,v)
lambdatext = [955 ' [nm]']; % The 955 is the unicode number for the lambda character. Because the editors of MATLAB versions prior to 2020a do not support unicode, we have to make the lambda in this sneaky way.
if src == v.h_centerbutton
set(v.h_slider,'Value',(numel(v.l)-1)/2 ... |
c9ed78d724287b07410cd3caa8a26ac1903fd74746116d4fb36eb032f8238003 | MATLAB | 2,539 | 94 | function cMap = makeColorMap(varargin)
%% MAKECOLORMAP makes smoothly varying colormaps
% a = makeColorMap(beginColor, middleColor, endColor, numSteps);
% a = makeColorMap(beginColor, endColor, numSteps);
% a = makeColorMap(beginColor, middleColor, endColor);
% a = makeColorMap(beginColor, endColor);
%
% all colors are... |
f61f7f460aac20f271dd7383e4c3015e71b2ae0f8a668c45d34f09c01da0ff48 | MATLAB | 2,541 | 83 | % Author: Birgit Nierula
% nierula@cbs.mpg.de
function bad_channels = prepro_check4badChannels(epo, trigger_name, wait4input, auto_badchan_labels)
%% check for bad channels
% input: epoched data
if ndims(epo.data) == 2
cnt = epo; clear epo
load([getenv('CFGDIR') 'cfg.mat'], 'iv_epoch', 'iv_baseline') % in ms
... |
31a639c0c7dc252c21fd6f0b1aa7ba464ece2ddcd82f733493ecc56b22927d84 | MATLAB | 2,542 | 47 | % SphericalMidPoint - Determine a point on a unit sphere by assuming
% equal distance to two spherical points
%
% (published in appendix of Kayser J, Tenke CE, Clin Neurophysiol 2006;117(2):348-368)
%
% Usage: [P] = SphericalPoint( Pl, Pr, Pm, P1, P2, lab);
%
% Implementation of simple linear... |
544f87b40cb8122a8e40320e54095c521fde5bd6d93f7362be6eda93e0ac38b5 | MATLAB | 2,542 | 68 | function imData=read_file(path_to_file,sframe,num2read,options)
% Reads uncompressed multipage .tiff, .hdf5, .avi or .raw files
% Usage: my_data=read_file('path_to_data_file, start frame, num to read);
% INPUTS:
% path_to_file: location of file to be read
% sframe: first frame to read (optional, defau... |
4393d7e69b2222ea7bd6c0aafa129adf36e60fb89be5e17305c939923ad04eba | MATLAB | 2,543 | 71 | %% SDO Optimization Wrapper
% Ad-hoc re-optimization of the SDO matrices, using the current SDOs as the
% initial values for optimization (sdo7).
%_______________________________________
% Copyright (C) 2023 Trevor S. Smith
% Drexel University College of Medicine
%
% This program is free software: you can redistribute... |
51d2ba7fb0fefe777329555809589386ebb7977b79369f85962f4be8da2a5205 | MATLAB | 2,543 | 86 | function [elem, points, surf_elem nnpe] = read_abaqus_inp_3D(mesh_fn)
% Reads abaqus mesh files exported by Mimics V.13
%
% Written by Hamid Ghadyani, Apr 2010
% The old version which is very slow is now called read_abaqus_inp_line
%
if(nargin~=1)
[fname,pname]=uigetfile('*.inp','Please pick the inp file');
else... |
9ec02f0734fc434cdfcac9be9b12849374a1d391d2f82e004bffabc65baa01df | MATLAB | 2,543 | 81 | function [event] = read_nexstim_event(filename)
% Use as
% [event] = read_nexstim_event(filename)
% Written by Vladimir Litvak based on the function nxeGetTriggers
% provided by Nexstim
%
% Copyright (C) 2007, Vladimir Litvak
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the document... |
9209e3335f7e07d751a7ef59b3eacdf349d0334903f9d2d5705e0e81bf0ca004 | MATLAB | 2,544 | 53 | function modelParam = set_depedent_parameters(modelParam, varargin)
% set_depedent_parameters.m
%
% Takes in "parameters" structure of initialized independent parameters and
% sets (or updates) all dependent parameters.
%
% Input:
% A parameters structure
%
% Output:
% The parameters structure with the dependent pa... |
fd9fc45f1c486cc54212235b809b3d7b315007a6531b5a3acfe3a85f8e54a7d3 | MATLAB | 2,544 | 87 | function fstats = lme_F(stats,C)
% fstats = lme_F(stats,C)
%
% Inference for the fixed-effects in the linear mixed-effects model(Depends
% on the Statistics toolbox).
%
% Input
% stats: Structure obtained from any of the model fitting functions:
% lme_fit_EM, lme_fit_FS and lme_fit_NR.
% C: Contrast matrix.
%
% Out... |
5c83c9e3bf1703d5c09260262c68d81c4a711faa57aad42901b1f362e59f261c | MATLAB | 2,545 | 100 | % Demo of factor analysis applied to binary newsgroups bag of words
% We compute 2d embedding
%PMTKreallySlow
% This file is from pmtk3.googlecode.com
requireStatsToolbox; % cmdscale
setSeed(0);
loadData('20news_w100');
% documents, wordlist, newsgroups, groupnames
wordocc = double(full(documents))'; % 16,642 docum... |
85a5f940d774e0b84ed1deaa71568b89365f91049641abf78c92aa17e9f1b91b | MATLAB | 2,545 | 85 | function [sel1, sel2] = match_str_lan(a, b);
% MATCH_STR looks for matching labels in two listst of strings
% and returns the indices into both the 1st and 2nd list of the matches.
% They will be ordered according to the first input argument.
%
% [sel1, sel2] = match_str(strlist1, strlist2)
%
% The strings can be stor... |
457e86308a1639e6676f228bb5ed95faebf510db47e5d5a73da62de5130b36b1 | MATLAB | 2,546 | 122 | load camera_results;
string_global = 'global n_ima';
for kk = 1:n_ima,
string_global = [string_global ' x_' num2str(kk) ' X_' num2str(kk) ' xproj_' num2str(kk) ' x_proj_' num2str(kk)];
end;
eval(string_global);
%----------------- global optimization: ---------------------
load projector_data; % load the proje... |
97abccf015d6380a6fb409c90857b5b7a55ba14c0085bad8943da623ce6fec80 | MATLAB | 2,546 | 75 | % Author: Birgit Nierula
% nierula@cbs.mpg.de
% Code adapted from Sencer Melih Deniz
function new = proc_tf_plots(epo, min_freq, max_freq, num_frex, chan_names, ...
color_range, is_normalized)
if ~isempty(chan_names)
%% select channels
chan_idx = find(ismember({epo.chanlocs.labels}, chan_names ));
epo... |
ca1a62bbd950403f13853c295f56a9c01928de25082cfc6a3295764f5798899d | MATLAB | 2,546 | 93 | function [ ival, pint ] = plane_normal_line_exp_int_3d ( pp, normal, p1, p2 )
%% PLANE_NORMAL_LINE_EXP_INT_3D intersection of plane and line in 3D.
%
% Discussion:
%
% The normal form of a plane in 3D is:
%
% PP is a point on the plane,
% N is a normal vector to the plane.
%
% The explicit form of a li... |
f121d8ff55bc8ff926327cde0ce55976afe36d0890bc87ded53fc53f650cc12b | MATLAB | 2,546 | 101 | % Measurement Error Compiling
%% ===== Data Compiling =====
% Use the first 3 sections to compile RMS error data from separate samples
% Then, run the following code to get RMS curve with SD shading.
%% Initialization: Run this section once
clear;
measData = struct([]);
%% Compiling: Run this section N times, for e... |
668b593bf014886e09a0d0db3dd9778030dabae9688a38f99331903ed7617e6f | MATLAB | 2,548 | 84 | function fig = plot_path(behavior,session,varargin)
% plots path in behavior.position by trial.
% LB 12/2022
% Input parser
p = inputParser;
p.addParameter('exclude_epoch', {'y_maze','sleep'});
p.parse(varargin{:});
exclude_epoch = p.Results.exclude_epoch;
if ~isfield(behavior,'trials')
error('No trials field ... |
ac8ffcc0a5e23e1aaf66672b735533369526a2b60f9a80d15b054ad561912c05 | MATLAB | 2,548 | 89 | function mergeDat = MergeTest2(spkDat, refClust, varargin)
spkDat.waves = double(spkDat.waves);
[wL, nChan, ~] = size(spkDat.waves);
pk = spkDat.peakLoc;
wP = spkDat.wavePad;
wL = wL - 2*wP;
clustList = setdiff(unique(spkDat.id), 0);
refIdx = find(clustList == refClust);
nClust = length(clustList);
win = 1000 * [1 - p... |
0aa91aab3b51596d3c8c8f66c07ac957e7013b621cd8704ecc8132c4bb150002 | MATLAB | 2,549 | 64 | function EWsig=McNemar_Figs3(dataOut,Bxname,IM,B,params)
% Plot network pairs meeting significance
if ~exist('B','var'),B=1;end
Pth=0.05./B;
PthMcN=0.05;
[NNidx,Tidx,TNidx]=IM2idx(IM);
Npairs=length(TNidx);
Nnets=max(IM.key(:,2));
NetKey=[[1:Nnets]',[1:Nnets]'];
%cMap=[1,1,1;0,0,0];
%% Significant stats by network b... |
637ed6895af76cf065ef98c9b8c112ffae73c550c9ca0aca6417569ccc8ad25e | MATLAB | 2,549 | 101 | function proc_createMixedLong(epo, fname, fpath, trigger_name, cond_name)
%% set max events
max_events = 2000; % mixed condition
% mixed
epo_long = get_getEpoStruct(epo, max_events, trigger_name{1});
%% save
d_idx = strfind(fname, cond_name);
ll = length(cond_name);
new_fname = [fname(1:d_idx+ll-1) '_long' fname(... |
15fec8998ab7100cfaee03567605173dcc71c342902b7fbc585ddc77d613b850 | MATLAB | 2,550 | 105 | %% Find Saccades and Microssacades in EyeLink Data
% Written by: Sharif I. Kronemer with open access scripts
% Last Modified: 9/22/2023
%% Saccade detection
% Calculate velocity/acceleration using 5-sample window
% (https://github.com/sj971/neurosci-saccade-detection/blob/master/analyzeEyeData.m)
% See Engbert and ... |
baca4c2deb6878d50700618206274dcb6d8928537c1c972df5b9dbd53055c488 | MATLAB | 2,550 | 93 | % Field Trip-related test scripts - Synthetic FT data - "Custom" - Detection.
%
%
% Includes.
% Assume that the parent called _init and _config.
%
%
% Event detection.
disp('== Detecting events using custom function.')
disp(sprintf( '-- (%dx%d patches)', ...
length(threshsweep_xy), length(threshsweep_xy) ));
d... |
3606fbb4c55e619b5269301b8dd78d772befa5bb6e0221093b4b2b58992569be | MATLAB | 2,551 | 84 | function [st,res,warningstr] = run(obj, varargin)
% Run a command using Matlab built-in system() command, but with some handy
% additional capabilities. (This is a replacement for the apt.syscmd()
% function, which dealt in raw strings.)
%
% Optional args allow caller to specify what to do if the command fails. (Can
... |
de23514200f66f4cbab85b72042754a15f92545ffa6c50b27e1470542a0813fe | MATLAB | 2,552 | 81 |
% distribute the convolution function, chunking to avoid GPU memory errors
function J = conv2_dist(filter, J, chunk_cols, gpu_strategy)
% FIXME gpu_chunks chosen arbitrarily to split convolution up
if ~gpu_strategy
gpu_strategy = 'single'
elseif ~strcmp(gpu_strategy, 'multi') && ~strcmp(gpu_strategy, 'single')
... |
8ce388b8ac1eb1ea4d1e753eb1d0e0dcb5010e5f46b9839f081d5ad6c6cd2f20 | MATLAB | 2,553 | 78 | function demoClassify
%DEMOCLASSIFY A demo used to test and demonstrate the usage of classifiers (clf*)
%
% To change the demo parameters alter this function. Note that the
% visualization of the train and test data may look different due to
% different 2D projections (see visualizeData).
%
% USAGE
% demoClassify
%
% ... |
9bfbb21ee2296b247f15b65b06efaccf4cd4004ad5c1e1c8374c45ede7b627a9 | MATLAB | 2,553 | 106 | function [E, yhat] = meg_objectiveFunction1_freeFreq(x,data,t,Fs,paramNames,fitType)
% Define objective function to minimize for fconmin/bads
% November 2023 KT
% Inputs:
% data: values by t, vector
% x: initial coefficients for search
% t: time vector
% Fs: sampling frequency, if not defined default to 1000 ... |
1d03227f647d86edc8d54e868f38e802db987faace25afef383c3a6423cc0786 | MATLAB | 2,554 | 67 | %-----------------------------------------------------------------------------------------
% Raster plot of amygdala neuron responding stronger
% to odors rated as liked vs. disliked
%
% Kehl et al. 2024 (DOI:XX)
% Single-Neuron Representations of Odors in the Human Brain
% Figure 4c
% Author: Marcel Kehl
% License... |
7da020100133869c0abd9856a2b206ab56764d38ac255167eb643fdbc186ea80 | MATLAB | 2,555 | 69 | %%Plots and calculates the mean bin value of all laps for data in each given task
%Chad Heer; Sheffield Lab
function [mean_lap_pupil, h, j] = plot_with_errorbars(lap_pupil, tasks, range, x_units)
%lap_pupil = pupil or fluorescence data organized in this format {task}(laps, mean pupil area in each bin)
%tasks = string... |
118f076d1da61e62041368f85de76d2765903b5c2d662dce3b05e6590f18031e | MATLAB | 2,556 | 85 | function [ data ] = shiftoffset_timelock( data, trials, offset, prestim, poststim, fsample, baseline)
% [ data ] = shiftoffset_timelock( data, trials, offset, prestim, poststim, fsample, baseline)% Anne Urai
warning off;
ft_defaults;
pupilchan = find(strcmp(data.label, 'EyePupil')==1);
if baseline == 2, % t... |
6aec860e22081c2b479b2a0921772ec25d31e043a665b1837887892f1fb8e073 | MATLAB | 2,556 | 50 | function r = calc_mouse_estimate_all_stages(all_learning_stages,simParam,nbootstrap_samples,rescale_to_target_distance,start_site,target_site)
if (nargin < 3) || isempty(nbootstrap_samples)
nbootstrap_samples = 10;
end
if (nargin < 4) || isempty(rescale_to_target_distance)
rescale_to_target... |
f3bb0d0b995455a51c9bd592bd43746a85425653f117020296a14bc431eef8b3 | MATLAB | 2,557 | 56 | function test_autotune_no_duplicate_align_entry()
% Test that the "Align using tail->head body axis" parameter
% (ROOT.MultiAnimal.TargetCrop.AlignUsingTrxTheta) appears exactly once
% in the Auto-tune tab of the training-parameters dialog for a bottom-up
% multi-animal project. It used to be rendered twice: once as a... |
889fe71e5b2888986f08c3a3ba6cc7372e4f1d739947ed2dd1981d8eff984dfe | MATLAB | 2,558 | 82 |
thresh_hold_percent_0 =0.15;
fititing_profile = 0.8;
intensity_profile_max = 0;
for kk = find([stitching_queue(:).max_direction] == 1)
intensity_profile_max = max([intensity_profile_max,intensity_profile{kk}]) ;
end
shifting_key = {};
for kk = find([stitching_queue(:).max_direction] == 1)
temp... |
b0f95674376c8890855e4698f03ff61645862ca89e546341ee2706ec596911ed | MATLAB | 2,560 | 102 | function varargout = unitTest(fname, varargin)
%% Run all of the demos that depend on fname.
%
%% Inptus
%
% fname - the name of the function, e.g. 'minFunc'.
%
%% Optional named inputs [default]
%
% 'run' - [true] run the demos instead of just returing their names
% 'recursive' - [true] include long ra... |
c722a42ad897ff068f9e89eeffa4e9a02a27bd6bb1801669da0a80487c10cdba | MATLAB | 2,560 | 99 | %%% This script alets the user enter the name of the images (base name, numbering scheme,...
% Checks that there are some images in the directory:
l_ras = dir('*ras');
s_ras = size(l_ras,1);
l_bmp = dir('*bmp');
s_bmp = size(l_bmp,1);
l_tif = dir('*tif');
s_tif = size(l_tif,1);
l_pgm = dir('*pgm');
s_pgm = siz... |
f06c38b058e778a65a075118de53a35b5a5183ae6ec5450153db31e197656ba1 | MATLAB | 2,560 | 63 | function EWsig=McNemar_Figs2(dataOut,IM,B,params)
% Plot network pairs meeting significance
if ~exist('B','var'),B=1;end
Pth=0.05./B;
PthMcN=0.05;
[NNidx,Tidx,TNidx]=IM2idx(IM);
Npairs=length(TNidx);
Nnets=max(IM.key(:,2));
NetKey=[[1:Nnets]',[1:Nnets]'];
%cMap=[1,1,1;0,0,0];
%% Significant stats by net... |
70a0be3794ce66c6797b686667cbb36d760c12923232faf90f1e2784d5b128e7 | MATLAB | 2,561 | 90 | function [out] = get_VolterraInGames(u,tau,param)
% estimate 1st-order Volterra Kernels of agents engaging in games
% FORMAT: [out] = get_VolterraKernels(u,tau,param)
% Volterra kernels can be either estimated in a non-parametric way, or in a
% parametric way (where kernels are assumed to be exponentially decaying
% wi... |
5d02e005e1f61479917c1fe0c67f3606a6bdba3f4cfc1c01ca141ea9df123373 | MATLAB | 2,562 | 96 | function [zones] = createZones(origin, diameter,varargin)
%This function creates pie shpaed quadrants for beahvioral testing in circular apparatus
%by LB & MG March 2019
%Input:
% origin: 1x2 matrix of xy coords for origin, ex: [0,0] for
% coordinates centered at 0,0.
% diameter: scalar quantity that... |
10db8ec5489cdba6e79ee82667d7d17ba5f235bce125a619b75385bbf33489b1 | MATLAB | 2,564 | 80 | function result = doinheritance(r, tr)
import yaml.*;
if ~exist('tr','var')
tr = r;
end;
result = recurse(r, 0, {tr});
end
function result = recurse(data, level, addit)
import yaml.*;
if iscell(data) && ~ismymatrix(data)
result = iter_cell(data, level, addit);
elseif isstruct(data)
r... |
888a614f940b9313a0b326f929e26ddc2d629c7e33189fa1cc462f2114fa3794 | MATLAB | 2,564 | 70 | %% 2D Gaussian contour plot along with its 1D marginals and conditionals.
%
%%
% This file is from pmtk3.googlecode.com
function gauss2dMargCondPlot()
fig = figure('Color','w');
mu = [0.5 0.5];
sigma = [0.018 0.01 ; 0.01 0.011];
plot2d();
plotMarginal();
plotConditional();
annotate();
function plot2d()
... |
9dca916b83609c877b6bf70da49e3ab7ff5b8f87d959c3218f0de659881be76b | MATLAB | 2,564 | 77 | function [MergedStack] = StackMerge(FileID,Stack1_Input,Stack2_Input,Limits)
%this will load in two stacks and merge them vertically and help avoid
%memory loading issues if large stacks
if length(Limits)~=1
Stack1=load(FileID,Stack1_Input);
Stack1_Name = fieldnames(Stack1);
Stack1 = Stack1.(Stack1_Na... |
255b1f3c33e5ec62b084183dd08531a329a54bc558be348d69a917d8161b18f6 | MATLAB | 2,565 | 95 | % This script gives the creation of the gaussian spheres used in the
% example, as well as its chi functions.
addpath('utilities', 'Sensitivities','Inverse');
do_save = 1; % 1 if save the data to .mat
%% ====== 'gauss1' ======
tag = 'gauss1';
cfg = getParams(tag);
if cfg.mask_number == 0 % no mask is used in this cas... |
3e0fe5e175d26f689d831621c49c24d8d0294b6f20596f86b3cf1ee0e6669090 | MATLAB | 2,565 | 101 | clear
close all
clc
%% Load data
addpath('/Users/jstrohl/Desktop/20231108 Strohl Sepsis fear network/materials/')
[num,txt,raw] = xlsread('20240519 PET LS data for ML.xlsx')
%% Import data
group = categorical(raw(2:end,1));
pet_data = cell2mat(raw(2:end,4:end));
pet_labels = raw(3:end);
% Label dataset
true_label... |
f48ef4a0fd24f99b89ddfcd259514bea351539745be00b8c72f16871968ac488 | MATLAB | 2,566 | 73 | % FT_POSTAMBLE_SAVEVAR is a helper script that optionally saves the output
% FieldTrip data structures to a *.mat file on disk. This is useful for
% batching and for distributed processing. This makes use of the
% cfg.outputfile variable.
%
% Use as
% ft_postamble savevar data
% ft_postamble savevar source mri
%
% ... |
8cdd477b8aed6b115c286bc3c540a9442d6b52d3329a61e99026d69289810b9a | MATLAB | 2,567 | 103 | %% demo of mixture of linear regression experts in 1d
% This file is from pmtk3.googlecode.com
clear all
close all
setSeed(0);
%data = load('mixexp_data.txt'); % data from Mike Jordan's homework
datasource = 3;
switch datasource
case 1,
xtrain = linspace(-1,1,200);
Ntrain = numel(xtrain);
ndx = (xtra... |
8cefa525b93cf81e16ca8b6a871dae559a046114c8c8bd8ab19fc3770c6b7bb7 | MATLAB | 2,567 | 76 | %% pipeline from MB modelling analysis:
% from calcium imaging timeseries to kenyon cells timeseries
% by A. Wystrach and M. Paoli, eLife 2024
close all, clear all, clc
% FUNCTIONS REQUIRED: create_MB, use_MB
%% load and extract database
load('examplary_bee.mat')
bee = database.bee;
bee = squeeze(mean(... |
275a13b0af7aa799113814e2e50b144e8abf71d56252fb8483ec9820039f209a | MATLAB | 2,568 | 89 | %% autocov_to_mvgc
%
% Calculate conditional time-domain MVGC (multivariate Granger causality)
%
% <matlab:open('autocov_to_mvgc.m') code>
%
%% Syntax
%
% F = autocov_to_mvgc(G,x,y)
%
%% Arguments
%
% See also <mvgchelp.html#4 Common variable names and data structures>.
%
% _input_
%
% G autocovariance... |
52dd8f0dd5a6faaa874f3c910111ba02416ed3341ffcd1fa9c96c709117535ae | MATLAB | 2,568 | 103 | function [mask_cluster_bg,centroids] = generate_BG_tissue_mask(anatomy,PET_dyn_path,hemi_scan,K,out_path, qc_path, mask_path, options)
if nargin<7
options=get_default_options();
end
NII_mask = load_nii(fullfile(mask_path,[anatomy '_mask.nii']));
mask = NII_mask.img;
%loading dynPET
[~, PET2D,... |
89af5f5209bcebcb8217631e9168c571e2d0f07acf7a292b893a606c5f2efd55 | MATLAB | 2,568 | 60 | function [ titleStr, settings, results ] = deleteLabels( dataview, settings )
% This function removes one or more variables from the datasource.
%
%
%
%<PRE>
% This file is part of dspace-core.
%
% Copyright (C) 2020 University Zurich, Sepp Kollmorgen
%
% This program is free... |
f1c1195e8b5b05d43b9b5abbabfaea3276a1d9176accc2d0edd59df7b3b64581 | MATLAB | 2,568 | 107 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
0e16cae69049efe55a1906e269595626fe05ecda20b236f890e955ffd42a53da | MATLAB | 2,569 | 72 | function [total_ST_resolution, total_power_captured, txt_han]= get_STresolution(stim_env, fs, dam_traj_Hz, tWindow, do_plot_boxes)
stimdur= length(stim_env)/fs;
freq_res_default= 1/tWindow;
nSegs= floor(stimdur/tWindow);
min_power_ratio= 0.95;
current_pow_box= nan(nSegs, 1);
current_pow_total= nan(nSegs, 1);
all_fre... |
2815b745456e96f902f971398bb2ab36fc1a60520cfdfc866b77003ffa7b218d | MATLAB | 2,569 | 118 | function [X_ind, X3d] = dummyEncoding(X, nStates)
% Convert a matrix of categorical features to binary form
% Each X(:, j) is expanded into a binary matrix of size n-by-nStates(j).
% These matrices are then concatinated horizontally forming an
% n-by-sum(nStates) binary matrix.
% if requested.
% X3d has form X(n,j,v) w... |
4de49c914309f8846f98254f5bcbe03ccd603dcfb894faaf970938a2bba182a4 | MATLAB | 2,569 | 100 | function [model, path] = logregFitPathCv(X, y, varargin)
% Fit a regularization path for logistic regression model
% using L1 or L2 regularizer and then pick best model.
% Also return params on the path.
% (This is a wrapper to the glmnet package.)
% INPUTS
% X ... N*D design matrix
% y ... N*... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.